HLA typing by SMRT DNA sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21509 | ENA |
REPOSITORIES: ENA
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Project description:HLA typing of 96 samples in one run of the Illumina MiSeq
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Project description:A targeted RNA-based method for typing of 12 classical HLA genes using Oxford Nanopore sequencing. In the method, were enriched HLA genes from cDNA of 50 individuals using gene-specific reverse primers. The library molecules were then barcoded, pooled into 2 separate gene pools, and sequenced on MinION R9.4 SpotON flow cells.
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Project description:Single molecule real-time (SMRT) DNA sequencing of HLA genes
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Project description:Gene products from the highly variable major histocompatibility locus, including HLA, are essential for self-recognition and immune surveillance of malignancy. Following allogeneic hematopoietic cell transplantation (alloHCT), genetic and epigenetic alterations in HLA can drive disease recurrence, making precise HLA assessment critical for determination of future therapy. However, current methods lack the sensitivity to quantify HLA transcripts at the single cell level, limiting their clinical utility. We introduce scrHLA-typing, a novel method that accurately identifies and quantifies HLA transcripts in single cells using hybridization capture and long-read sequencing. When applied to samples from patients with post-transplant relapse, scrHLA-typing successfully detected allele-specific expression of MHC gene products at clinically actionable levels. By characterizing allele expression in residual leukemia cells, our assay identified differences in expression patterns among patients. This capability highlights scrHLA-typing’s potential to improve risk stratification and guide the selection of appropriate salvage therapies, enhancing personalized treatment strategies after post-transplant relapse.
2025-09-17 | GSE305306 | GEO
Project description:Gene products from the highly variable major histocompatibility locus, including HLA, are essential for self-recognition and immune surveillance of malignancy. Following allogeneic hematopoietic cell transplantation (alloHCT), genetic and epigenetic alterations in HLA can drive disease recurrence, making precise HLA assessment critical for determination of future therapy. However, current methods lack the sensitivity to quantify HLA transcripts at the single cell level, limiting their clinical utility. We introduce scrHLA-typing, a novel method that accurately identifies and quantifies HLA transcripts in single cells using hybridization capture and long-read sequencing. When applied to samples from patients with post-transplant relapse, scrHLA-typing successfully detected allele-specific expression of MHC gene products at clinically actionable levels. By characterizing allele expression in residual leukemia cells, our assay identified differences in expression patterns among patients. This capability highlights scrHLA-typing’s potential to improve risk stratification and guide the selection of appropriate salvage therapies, enhancing personalized treatment strategies after post-transplant relapse.
2025-09-17 | GSE305305 | GEO
Project description:Gene products from the highly variable major histocompatibility locus, including HLA, are essential for self-recognition and immune surveillance of malignancy. Following allogeneic hematopoietic cell transplantation (alloHCT), genetic and epigenetic alterations in HLA can drive disease recurrence, making precise HLA assessment critical for determination of future therapy. However, current methods lack the sensitivity to quantify HLA transcripts at the single cell level, limiting their clinical utility. We introduce scrHLA-typing, a novel method that accurately identifies and quantifies HLA transcripts in single cells using hybridization capture and long-read sequencing. When applied to samples from patients with post-transplant relapse, scrHLA-typing successfully detected allele-specific expression of MHC gene products at clinically actionable levels. By characterizing allele expression in residual leukemia cells, our assay identified differences in expression patterns among patients. This capability highlights scrHLA-typing’s potential to improve risk stratification and guide the selection of appropriate salvage therapies, enhancing personalized treatment strategies after post-transplant relapse.
2025-09-17 | GSE305307 | GEO
Project description:DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates
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Project description:Genomic DNA contains next to the four canonical nucleosides dA, dC, dG and T the additional base 5-methyldeoxycytidine (mdC). The presence of this methylated cytidine nucleoside in promoter regions or gene bodies has an instrumental effect on the transcriptional activity of the corresponding gene. The methylation patterns of genes are therefore responsible for either silencing or activation of genes. Sequencing of mdC positions in the genome is consequently of paramount importance for early cancer diagnostics in order to determine incorrect expression of genes. Today, the bisulfite method is the gold standard for mdC-sequencing, which has however the caveat that the majority of the input DNA is degraded during the bisulfite treatment. In addition, bisulfite sequencing is rather error prone. Here we report a benign, bisulfite free mdC sequencing method based on 3rd generation single molecule SMRT sequencing. The fundament of the technology is a new Tet3 enzyme that oxidizes mdCs with high efficiency to 5-carboxycytidine (cadC). caC in turn provides and excellent read out by SMRT sequencing using specially trained AI-based algorithms.
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